A NUCLEAR waste dump will almost certainly be built in the Territory after legislation passed through the Senate.

But Territory groups say they will keep fighting to stop the dump.

The Federal Government is only considering Muckaty Station - about 120km north of Tennant Creek - as a future site.

The Greens and independent senator Nick Xenophon opposed the National Radioactive Waste Management Bill, but NT senators, Labor's Trish Crossin and the Country Liberal party's Nigel Scullion, voted for it.

Environment Centre NT spokeswoman Cat Beaton said there would be a fight to stop the dump.

"Canberra may now have its legislation, but we are more determined than ever to ensure a radioactive waste dump doesn't end up in the Territory," she said.

"This legislation spits in the face of the NT Government who have legislated against a waste dump, Muckaty traditional owners who have consistently said no, and unions, church groups, green groups and Territorians who do not want the risks that come with a radioactive dump in their Territory."

Western Australian Greens senator Scott Ludlam had his amendment - which means it must return to the Lower House to be rubber stamped - passed, effectively barring any international radioactive waste from being stored at the dump unless it originated in Australia.

But he was not happy.

"I think what we saw today was an abomination," he said. "It was a shame on the Territory's representatives in the Parliament. You shouldn't need a guy from WA sticking up (for) the rights of the Territory."

A dispute over the land on which the dump could sit is before the Federal Court in Victoria. The case is expected to continue despite the legislation.

Federal Resources Minister Martin Ferguson told journalists the Federal Government would not proceed with the dump until the court case was decided.

Only the NT and federal governments will be allowed to send low-level waste free of charge, while other states will have to pay.